public class IdentificationParameters extends Object implements Serializable, MarshallableParameter
MarshallableParameter.Type
Constructor and Description |
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IdentificationParameters()
Creates empty identification parameters.
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IdentificationParameters(SearchParameters searchParameters)
Creates default identification parameters from the given search
parameters.
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IdentificationParameters(String name,
String description,
SearchParameters searchParameters,
AnnotationParameters annotationParameters,
SequenceMatchingParameters sequenceMatchingParameters,
PeptideVariantsParameters peptideVariantsParameters,
GeneParameters geneParameters,
PsmScoringParameters psmScoringParameters,
PeptideAssumptionFilter peptideAssumptionFilter,
ModificationLocalizationParameters ModificationLocalizationParameters,
ProteinInferenceParameters proteinInferenceParameters,
IdMatchValidationParameters idValidationParameters,
FractionParameters fractionParameters)
Constructor.
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Modifier and Type | Method and Description |
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boolean |
equals(IdentificationParameters otherIdentificationParameters)
Returns true if the identification parameter objects have identical
settings.
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AnnotationParameters |
getAnnotationParameters()
Returns the annotation parameters used for identification.
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static double |
getDaTolerance(double ppmTolerance,
double refMass)
Returns the absolute tolerance in Dalton corresponding to the relative
tolerance in ppm at the given reference mass.
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boolean |
getDefaultDescription()
Indicates whether the description is automatically generated.
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String |
getDescription()
Returns the description of the parameters.
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FractionParameters |
getFractionParameters()
Returns the fraction parameters.
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GeneParameters |
getGeneParameters()
Returns the gene parameters.
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static IdentificationParameters |
getIdentificationParameters(File identificationParametersFile)
Loads the identification parameters from a file.
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IdMatchValidationParameters |
getIdValidationParameters()
Returns the identification matches validation parameters.
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ModificationLocalizationParameters |
getModificationLocalizationParameters()
Returns the modification localization scoring parameters.
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String |
getName()
Returns the name of the parameters.
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PeptideAssumptionFilter |
getPeptideAssumptionFilter()
Returns the filter used when importing PSMs.
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PeptideVariantsParameters |
getPeptideVariantsParameters()
Returns the peptide variant parameters.
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static double |
getPpmTolerance(double daltonTolerance,
double refMass)
Returns the relative tolerance in ppm corresponding to the absolute
tolerance in Dalton at the given reference mass.
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ProteinInferenceParameters |
getProteinInferenceParameters()
Returns the protein inference parameters.
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PsmScoringParameters |
getPsmScoringParameters()
Returns the scoring parameters used when scoring PSMs.
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SearchParameters |
getSearchParameters()
Returns the parameters used for the spectrum matching.
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SequenceMatchingParameters |
getSequenceMatchingParameters()
Returns the sequence matching parameters.
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MarshallableParameter.Type |
getType()
Returns the type of marshalled parameter from an unmarshalled object.
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static void |
saveIdentificationParameters(IdentificationParameters identificationParameters,
File identificationParametersFile)
Saves the identification parameters to a file.
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void |
setAnnotationParameters(AnnotationParameters annotationParameters)
Sets the annotation parameters used for identification.
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void |
setDescription(String description,
boolean automaticallyGenerated)
Sets the description of the parameters.
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void |
setFractionParameters(FractionParameters fractionParameters)
Sets the fraction parameters.
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void |
setGeneParameters(GeneParameters geneParameters)
Sets the gene parameters.
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void |
setIdValidationParameters(IdMatchValidationParameters idValidationParameters)
Sets the identification matches validation parameters.
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void |
setModificationLocalizationParameters(ModificationLocalizationParameters modificationLocalizationParameters)
Sets the modification localization parameters.
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void |
setName(String name)
Sets the name of the parameters.
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void |
setParametersFromSearch(SearchParameters searchParameters)
Sets identification parameters based on given search parameters.
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void |
setPeptideAssumptionFilter(PeptideAssumptionFilter peptideAssumptionFilter)
Sets the filter used when importing PSMs.
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void |
setPeptideVariantsParameters(PeptideVariantsParameters peptideVariantsParameters)
Sets the peptide variant parameters.
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void |
setProteinInferenceParameters(ProteinInferenceParameters proteinInferenceParameters)
Sets the protein inference parameters.
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void |
setPsmScoringParameters(PsmScoringParameters psmScoringParameters)
Sets the scoring preferences used when scoring PSMs.
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void |
setSearchParameters(SearchParameters searchParameters)
Sets the parameters used for the spectrum matching.
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void |
setSequenceMatchingParameters(SequenceMatchingParameters sequenceMatchingParameters)
Sets the sequence matching preferences.
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void |
setType()
Sets the parameters type.
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public IdentificationParameters()
public IdentificationParameters(SearchParameters searchParameters)
searchParameters
- the search parameterspublic IdentificationParameters(String name, String description, SearchParameters searchParameters, AnnotationParameters annotationParameters, SequenceMatchingParameters sequenceMatchingParameters, PeptideVariantsParameters peptideVariantsParameters, GeneParameters geneParameters, PsmScoringParameters psmScoringParameters, PeptideAssumptionFilter peptideAssumptionFilter, ModificationLocalizationParameters ModificationLocalizationParameters, ProteinInferenceParameters proteinInferenceParameters, IdMatchValidationParameters idValidationParameters, FractionParameters fractionParameters)
name
- the name of the parametersdescription
- the descriptionsearchParameters
- the search parametersannotationParameters
- the annotation parameterssequenceMatchingParameters
- the sequence matching parameterspeptideVariantsParameters
- the peptide variant parametersgeneParameters
- the gene parameterspsmScoringParameters
- the PSM scoring parameterspeptideAssumptionFilter
- the peptide assumption filtersModificationLocalizationParameters
- the PTM localization scoring
parametersproteinInferenceParameters
- the protein inference parametersidValidationParameters
- the matches validation parametersfractionParameters
- the fraction parameterspublic SearchParameters getSearchParameters()
public void setSearchParameters(SearchParameters searchParameters)
searchParameters
- the parameters used for the spectrum matchingpublic static double getPpmTolerance(double daltonTolerance, double refMass)
daltonTolerance
- the absolute tolerance in DaltonrefMass
- the reference mass in Daltonpublic static double getDaTolerance(double ppmTolerance, double refMass)
ppmTolerance
- the absolute tolerance in ppmrefMass
- the reference mass in Daltonpublic AnnotationParameters getAnnotationParameters()
public void setAnnotationParameters(AnnotationParameters annotationParameters)
annotationParameters
- the annotation parameters used for
identificationpublic PeptideAssumptionFilter getPeptideAssumptionFilter()
public void setPeptideAssumptionFilter(PeptideAssumptionFilter peptideAssumptionFilter)
peptideAssumptionFilter
- the filter used when importing PSMspublic PsmScoringParameters getPsmScoringParameters()
public void setPsmScoringParameters(PsmScoringParameters psmScoringParameters)
psmScoringParameters
- the scoring preferences used when scoring
PSMspublic ModificationLocalizationParameters getModificationLocalizationParameters()
public void setModificationLocalizationParameters(ModificationLocalizationParameters modificationLocalizationParameters)
modificationLocalizationParameters
- the modification localization
parameterspublic SequenceMatchingParameters getSequenceMatchingParameters()
public void setSequenceMatchingParameters(SequenceMatchingParameters sequenceMatchingParameters)
sequenceMatchingParameters
- the sequence matching preferencespublic PeptideVariantsParameters getPeptideVariantsParameters()
public void setPeptideVariantsParameters(PeptideVariantsParameters peptideVariantsParameters)
peptideVariantsParameters
- the peptide variant parameterspublic IdMatchValidationParameters getIdValidationParameters()
public void setIdValidationParameters(IdMatchValidationParameters idValidationParameters)
idValidationParameters
- the identification matches validation
parameterspublic ProteinInferenceParameters getProteinInferenceParameters()
public void setProteinInferenceParameters(ProteinInferenceParameters proteinInferenceParameters)
proteinInferenceParameters
- the protein inference parameterspublic GeneParameters getGeneParameters()
public void setGeneParameters(GeneParameters geneParameters)
geneParameters
- the gene parameterspublic FractionParameters getFractionParameters()
public void setFractionParameters(FractionParameters fractionParameters)
fractionParameters
- the fraction parameterspublic static IdentificationParameters getIdentificationParameters(File identificationParametersFile) throws IOException, ClassNotFoundException
identificationParametersFile
- the fileIOException
- if an error occurs while reading the fileClassNotFoundException
- if the file could not be castedpublic static void saveIdentificationParameters(IdentificationParameters identificationParameters, File identificationParametersFile) throws IOException
identificationParameters
- the identification parametersidentificationParametersFile
- the fileIOException
- if an error occurred while writing the filepublic String getName()
public void setName(String name)
name
- the name of the parameterspublic String getDescription()
public boolean getDefaultDescription()
public void setDescription(String description, boolean automaticallyGenerated)
description
- the description of the parametersautomaticallyGenerated
- boolean indicating whether the description
is automatically generatedpublic void setParametersFromSearch(SearchParameters searchParameters)
searchParameters
- the parameters used for the searchpublic void setType()
MarshallableParameter
setType
in interface MarshallableParameter
public MarshallableParameter.Type getType()
MarshallableParameter
getType
in interface MarshallableParameter
public boolean equals(IdentificationParameters otherIdentificationParameters)
otherIdentificationParameters
- the parameters to compare toCopyright © 2018. All rights reserved.